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Yorodumi- PDB-2jal: Beta-glucosidase from Thermotoga maritima in complex with cycloph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jal | ||||||
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Title | Beta-glucosidase from Thermotoga maritima in complex with cyclophellitol | ||||||
Components | BETA-GLUCOSIDASE A | ||||||
Keywords | HYDROLASE / POLYSACCHARIDE DEGRADATION / GLYCOSIDASE / GLYCOSIDE HYDROLASE / CELLULOSE DEGRADATION / CARBOHYDRATE METABOLISM / FAMILY 1 / COVALENT / INHIBITOR | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gloster, T.M. / Madsen, R. / Davies, G.J. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2007 Title: Structural Basis for Cyclophellitol Inhibition of a Beta-Glucosidase. Authors: Gloster, T.M. / Madsen, R. / Davies, G.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jal.cif.gz | 202.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jal.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 2jal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/2jal ftp://data.pdbj.org/pub/pdb/validation_reports/ja/2jal | HTTPS FTP |
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-Related structure data
Related structure data | 1od0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.006987, -0.9904, -0.1382), Vector: |
-Components
#1: Protein | Mass: 53940.648 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-446 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q08638, beta-glucosidase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE CRYSTALLIZED CONTAINS AN N-TERMINAL HIS TAG FROM THE EXPRESSION VECTOR. NUMBERING ...THE SEQUENCE CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL. |
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Crystal grow | pH: 7 Details: 10 MG/ML PROTEIN. 15% PEG 4K, 0.1 M IMIDAZOLE, 0.2 M CALCIUM ACETATE., pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9788 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 30, 2006 / Details: SILICON TOROIDAL MIRROR COATED WITH RHODIUM |
Radiation | Monochromator: SILICON (1 1 1) CHANNEL- CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 76161 / % possible obs: 94.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5 / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OD0 Resolution: 1.9→72.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.973 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→72.74 Å
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